OK the gems make more sense now with how they work. It works better. And now Haruza not needing to study the bodies makes sense. So I can't see any holes in that right now.

Your new spoiler gives information to move the plot along. It gives Magma a reason to attack Haruza and a reason for Haruza and the trainer (in case you change his name) to chase down Magam to stop them from creating a stronger Pokemon.

Quote:

such as mew(Mewtwo was made up of a trace of mew), or Ho-Oh?(I could have sworn there was an item in game that was Ho-Oh's feathers or something similar.). Heck, even finding Kyogre, Rayquaza, and Groudon and mixing their DNA into one body,

I know that Ho-Oh and Lugia have their feathers from the games/anime. (The silver feather from Lugia is actually a big item to move my own fics' plot along.) You could maybe make use of the Red, Blue, and Jade Orbs (the summoning items in the games) for Groudon, Kyogre, and Rayquaza for their DNA. The orbs are said to contain an ancient power, and they summon the respective Pokemon (and possibly control them which I think happens in the anime?). Magma (and maybe Aqua) could go after those items.

Spoiler:

But yeah, when Haruza and the trainer stop Magma from using the gems, they could think that their goal was too big for them to handle and go back to just chasing after Groudon. That would leave you open for allowing the events of R/S/E to happen so you'd be okay there.

I think you've got enough to get the beginning written out. Good luck!

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Now nobody, nobody, nobody, nobody speaks my name
I'm just another blister in the mouth of shame
A bug in Ender's Game